Furious Blackpool supporters pelted the directors' box and main reception area at Bloomfield Road with a flare, a smoke bomb, fireworks and eggs before their 1-1 draw with Reading on Tuesday.
The bottom-of-the-table Seasiders' relegation to League One was sealed by Rotherham's victory over Brighton on Monday, a result that condemned them to the third tier with six games of their season still to spare, and supporters vented their frustration before Tuesday's game.
Chairman Karl Oyston was the target of their criticism as supporters congregated in front of the West Stand to demonstrate against their owner before the directors' box windows were targeted with eggs.
Disgruntled fans chanted "Oyston out" and "We're relegated because of your greed" before a flare, a smoke bomb and fireworks were thrown into the cordoned-off area in front of the main entrance.
Stewards and police were present but the protests did not spill over into violence.
Clark acknowledged that a "horrendous season" had contributed to the swathes of empty seats at recent home matches but is hopeful of winning back those disillusioned fans by rebuilding his squad over the summer.
"We're down a level and that's going to be hard," he said of getting fans back through the turnstiles at Bloomfield Road.
"We've obviously had a horrendous season to put up with, but if we do it right with our recruitment process over the summer, we do things in the right way and get the right type of players in -- then they can come and watch us over the pre-season and see a new group of players that they can get excited about that we can get them back on to the seats.
"The only way we can do that is by getting a group together that's going to give us a fighting chance to get back up and we hit the ground running at the start of the season."